Examples with ShrimpDataFileInterface org.cirdles.squid.shrimp.ShrimpDataFileInterface used on opensource projects

Example 1 with ShrimpDataFileInterface

use of org.cirdles.squid.shrimp.ShrimpDataFileInterface in project Squid by CIRDLES.

the class OPFileHandler method convertOPFilesToPrawnFile.

private ShrimpDataFileInterface convertOPFilesToPrawnFile(List<OPFraction> opFractions) {
    ShrimpDataFileInterface prawnFile = new PrawnFile();
    prawnFile.setSoftwareVersion("Squid3 v" + Squid.VERSION + "-processed OP File");
    for (OPFraction opFraction : opFractions) {
        PrawnFile.Run run = new PrawnFile.Run();
        // run
        // run parameters
        PrawnFile.Run.Par title = new PrawnFile.Run.Par();
        title.setName(RunParameterNames.TITLE);
        title.setValue(opFraction.getName());
        run.getPar().add(title);
        PrawnFile.Run.Par sets = new PrawnFile.Run.Par();
        sets.setName(RunParameterNames.SETS);
        sets.setValue("" + opFraction.getSets());
        run.getPar().add(sets);
        PrawnFile.Run.Par measurements = new PrawnFile.Run.Par();
        measurements.setName(RunParameterNames.MEASUREMENTS);
        measurements.setValue("" + opFraction.getMeasurements());
        run.getPar().add(measurements);
        PrawnFile.Run.Par scans = new PrawnFile.Run.Par();
        scans.setName(RunParameterNames.SCANS);
        scans.setValue("" + opFraction.getScans());
        run.getPar().add(scans);
        PrawnFile.Run.Par deadTimeNS = new PrawnFile.Run.Par();
        deadTimeNS.setName(RunParameterNames.DEAD_TIME_NS);
        deadTimeNS.setValue("0");
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        PrawnFile.Run.Par sbmZeroCps = new PrawnFile.Run.Par();
        sbmZeroCps.setName(RunParameterNames.SBM_ZERO_CPS);
        sbmZeroCps.setValue("" + opFraction.getSbmZeroCPS());
        run.getPar().add(sbmZeroCps);
        // need placeholders
        /*
            <par name="autocentering" value="yes" />
            <par name="qt1y_mode" value="qt1y_scan" /><!-- can be "focus_stage" "qt1y_scan" "constant" -->
            <par name="deflect_beam_between_peaks" value="yes" />
            <par name="autocenter_method" value="50_percent_pk_height" /><!-- can be "polynomial_fit" "50_percent_pk_height" "sliding_integral" -->
            <par name="stage_x" value="4927" />
            <par name="stage_y" value="14867" />
            <par name="stage_z" value="7415" />
             */
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // placeholder in Par list
        run.getPar().add(deadTimeNS);
        // run.runtable
        // run.runtable entries
        // run.runtable entry parameters
        run.setRunTable(new PrawnFile.Run.RunTable());
        for (int i = 0; i < opFraction.getCountTimeSec().length; i++) {
            PrawnFile.Run.RunTable.Entry entry = new PrawnFile.Run.RunTable.Entry();
            // the first two are faked for now
            PrawnFile.Run.RunTable.Entry.Par label = new PrawnFile.Run.RunTable.Entry.Par();
            label.setName(RunTableEntryParameterNames.LABEL);
            int measCount = opFraction.getMeasurements();
            label.setValue((measCount == 9) ? massStationLabelsNINE[i] : (measCount == 10) ? massStationLabelsTEN[i] : massStationLabelsELEVEN[i]);
            entry.getPar().add(label);
            PrawnFile.Run.RunTable.Entry.Par amu = new PrawnFile.Run.RunTable.Entry.Par();
            amu.setName(RunTableEntryParameterNames.AMU);
            amu.setValue((measCount == 9) ? massStationAMUsNINE[i] : (measCount == 10) ? massStationAMUsTEN[i] : massStationAMUsELEVEN[i]);
            entry.getPar().add(amu);
            // need placeholder parameters for
            /*
                <par name="trim_amu" value="0.000" />
                <par name="autocenter_offset_amu" value="0.000000" /><!-- 0=do not use -->
                 */
            PrawnFile.Run.RunTable.Entry.Par placeHolderPar = new PrawnFile.Run.RunTable.Entry.Par();
            entry.getPar().add(placeHolderPar);
            entry.getPar().add(placeHolderPar);
            PrawnFile.Run.RunTable.Entry.Par countTimeSec = new PrawnFile.Run.RunTable.Entry.Par();
            countTimeSec.setName(RunTableEntryParameterNames.COUNT_TIME_SEC);
            countTimeSec.setValue("" + opFraction.getCountTimeSec()[i]);
            entry.getPar().add(countTimeSec);
            // need placeholder parameters for
            /*
                <par name="delay_sec" value="5.000" />
                <par name="collector_focus" value="18.000" />
                 */
            entry.getPar().add(placeHolderPar);
            entry.getPar().add(placeHolderPar);
            PrawnFile.Run.RunTable.Entry.Par centeringTimeSec = new PrawnFile.Run.RunTable.Entry.Par();
            centeringTimeSec.setName(RunTableEntryParameterNames.CENTERING_TIME_SEC);
            centeringTimeSec.setValue("0");
            entry.getPar().add(centeringTimeSec);
            run.getRunTable().getEntry().add(entry);
        }
        // run.set
        // run.set parameters
        // run.set.scan
        // run.set.scan.measurement
        // run.set.scan.measurement.parameters
        // run.set.scan.measurement.data
        run.setSet(new PrawnFile.Run.Set());
        PrawnFile.Run.Set.Par date = new PrawnFile.Run.Set.Par();
        date.setName(SetParameterNames.DATE);
        date.setValue(new Date(opFraction.getDateTimeMilliseconds()).toString());
        run.getSet().getPar().add(date);
        PrawnFile.Run.Set.Par time = new PrawnFile.Run.Set.Par();
        time.setName(SetParameterNames.TIME);
        time.setValue(new Time(opFraction.getDateTimeMilliseconds()).toString());
        run.getSet().getPar().add(time);
        for (int j = 0; j < opFraction.getScans(); j++) {
            PrawnFile.Run.Set.Scan scan = new PrawnFile.Run.Set.Scan();
            for (int i = 0; i < opFraction.getMeasurements(); i++) {
                PrawnFile.Run.Set.Scan.Measurement measurement = new PrawnFile.Run.Set.Scan.Measurement();
                // need placeholder
                /*
                    <par name="detectors" value="12" />
                     */
                PrawnFile.Run.Set.Scan.Measurement.Par placeHolderPar = new PrawnFile.Run.Set.Scan.Measurement.Par();
                measurement.getPar().add(placeHolderPar);
                PrawnFile.Run.Set.Scan.Measurement.Par trimMass = new PrawnFile.Run.Set.Scan.Measurement.Par();
                trimMass.setName("trim_mass");
                trimMass.setValue("0");
                measurement.getPar().add(trimMass);
                PrawnFile.Run.Set.Scan.Measurement.Par timeStampSec = new PrawnFile.Run.Set.Scan.Measurement.Par();
                timeStampSec.setName("time_stamp_sec");
                timeStampSec.setValue("" + opFraction.getTimeStampSec()[i][j]);
                measurement.getPar().add(timeStampSec);
                PrawnFile.Run.Set.Scan.Measurement.Data totalCounts = new PrawnFile.Run.Set.Scan.Measurement.Data();
                // TODO: make robust
                if (opFraction.getMeasurements() == 10) {
                    totalCounts.setName(massStationLabelsTEN[i]);
                } else {
                    totalCounts.setName(massStationLabelsELEVEN[i]);
                }
                // place negative total in the measurements slot as a signal flag "OP FILE" to PrawnFileRunParser
                totalCounts.setValue("-" + opFraction.getTotalCounts()[i][j]);
                measurement.getData().add(totalCounts);
                PrawnFile.Run.Set.Scan.Measurement.Data totalSBM = new PrawnFile.Run.Set.Scan.Measurement.Data();
                totalSBM.setName("SBM");
                totalSBM.setValue("" + opFraction.getTotalSBM()[i][j]);
                measurement.getData().add(totalSBM);
                scan.getMeasurement().add(measurement);
            }
            run.getSet().getScan().add(scan);
        }
        prawnFile.getRun().add(run);
    }
    prawnFile.setRuns((short) opFractions.size());
    return prawnFile;
}

Example 2 with ShrimpDataFileInterface

use of org.cirdles.squid.shrimp.ShrimpDataFileInterface in project Squid by CIRDLES.

the class OPFileHandler method convertOPFileToPrawnFile.

public ShrimpDataFileInterface convertOPFileToPrawnFile(File opFile) {
    List<OPFraction> opFractions = OPFileRunFractionParser.parseOPFile(opFile);
    ShrimpDataFileInterface prawnFile = convertOPFilesToPrawnFile(opFractions);
    return prawnFile;
}

Example 3 with ShrimpDataFileInterface

use of org.cirdles.squid.shrimp.ShrimpDataFileInterface in project Squid by CIRDLES.

the class PrawnLegacyFileHandler method convertPrawnLegacyFileToPrawnFile.

public static ShrimpDataFileInterface convertPrawnLegacyFileToPrawnFile(ShrimpDataLegacyFileInterface prawnLegacyFile) {
    ShrimpDataFileInterface prawnFile = new PrawnFile();
    prawnFile.setSoftwareVersion("Squid3 v" + Squid.VERSION + " - translated from SHRIMP II v2 SW");
    prawnFile.setRuns((short) prawnLegacyFile.getRun().size());
    for (PrawnLegacyFile.Run legacyRun : prawnLegacyFile.getRun()) {
        PrawnFile.Run run = new PrawnFile.Run();
        // run
        // run parameters
        PrawnFile.Run.Par title = new PrawnFile.Run.Par();
        title.setName(RunParameterNames.TITLE);
        title.setValue(legacyRun.getTitle());
        run.getPar().add(title);
        PrawnFile.Run.Par sets = new PrawnFile.Run.Par();
        sets.setName(RunParameterNames.SETS);
        sets.setValue("" + legacyRun.getSets());
        run.getPar().add(sets);
        PrawnFile.Run.Par measurements = new PrawnFile.Run.Par();
        measurements.setName(RunParameterNames.MEASUREMENTS);
        measurements.setValue("" + legacyRun.getPeaks());
        run.getPar().add(measurements);
        PrawnFile.Run.Par scans = new PrawnFile.Run.Par();
        scans.setName(RunParameterNames.SCANS);
        scans.setValue("" + legacyRun.getScans());
        run.getPar().add(scans);
        PrawnFile.Run.Par deadTimeNS = new PrawnFile.Run.Par();
        deadTimeNS.setName(RunParameterNames.DEAD_TIME_NS);
        deadTimeNS.setValue("" + legacyRun.getDeadTimeNs());
        run.getPar().add(deadTimeNS);
        PrawnFile.Run.Par sbmZeroCps = new PrawnFile.Run.Par();
        sbmZeroCps.setName(RunParameterNames.SBM_ZERO_CPS);
        sbmZeroCps.setValue("" + legacyRun.getSbmZeroCps());
        run.getPar().add(sbmZeroCps);
        PrawnFile.Run.Par autocentering = new PrawnFile.Run.Par();
        autocentering.setName(RunParameterNames.AUTOCENTERING);
        autocentering.setValue("" + legacyRun.getAutocentering());
        run.getPar().add(autocentering);
        PrawnFile.Run.Par qt1y_mode = new PrawnFile.Run.Par();
        qt1y_mode.setName(RunParameterNames.QT_1_Y_MODE);
        qt1y_mode.setValue("" + legacyRun.getQt1YMode());
        run.getPar().add(qt1y_mode);
        PrawnFile.Run.Par deflect_beam_between_peaks = new PrawnFile.Run.Par();
        deflect_beam_between_peaks.setName(RunParameterNames.DEFLECT_BEAM_BETWEEN_PEAKS);
        deflect_beam_between_peaks.setValue("" + legacyRun.getDeflectBeamBetweenPeaks());
        run.getPar().add(deflect_beam_between_peaks);
        PrawnFile.Run.Par autocenter_method = new PrawnFile.Run.Par();
        autocenter_method.setName(RunParameterNames.AUTOCENTER_METHOD);
        autocenter_method.setValue("" + legacyRun.getAutocenterMethod());
        run.getPar().add(autocenter_method);
        // need placeholders for stage x,y,z
        PrawnFile.Run.Par stage_x = new PrawnFile.Run.Par();
        stage_x.setName(RunParameterNames.STAGE_X);
        stage_x.setValue("0");
        run.getPar().add(stage_x);
        PrawnFile.Run.Par stage_y = new PrawnFile.Run.Par();
        stage_y.setName(RunParameterNames.STAGE_Y);
        stage_y.setValue("0");
        run.getPar().add(stage_y);
        PrawnFile.Run.Par stage_z = new PrawnFile.Run.Par();
        stage_z.setName(RunParameterNames.STAGE_Z);
        stage_z.setValue("0");
        run.getPar().add(stage_z);
        // run.runtable
        // run.runtable entries
        // run.runtable entry parameters
        run.setRunTable(new PrawnFile.Run.RunTable());
        for (int i = 0; i < legacyRun.getRunTable().getName().size(); i++) {
            PrawnFile.Run.RunTable.Entry entry = new PrawnFile.Run.RunTable.Entry();
            PrawnLegacyFile.Run.RunTable legacyRunTable = legacyRun.getRunTable();
            PrawnFile.Run.RunTable.Entry.Par label = new PrawnFile.Run.RunTable.Entry.Par();
            label.setName(RunTableEntryParameterNames.LABEL);
            label.setValue("" + legacyRunTable.getName().get(i));
            entry.getPar().add(label);
            PrawnFile.Run.RunTable.Entry.Par amu = new PrawnFile.Run.RunTable.Entry.Par();
            amu.setName(RunTableEntryParameterNames.AMU);
            amu.setValue("" + legacyRunTable.getTrimMass().get(i));
            entry.getPar().add(amu);
            PrawnFile.Run.RunTable.Entry.Par trim_amu = new PrawnFile.Run.RunTable.Entry.Par();
            trim_amu.setName(RunTableEntryParameterNames.TRIM_AMU);
            trim_amu.setValue("0.0");
            entry.getPar().add(trim_amu);
            PrawnFile.Run.RunTable.Entry.Par autocenter_offset_amu = new PrawnFile.Run.RunTable.Entry.Par();
            autocenter_offset_amu.setName(RunTableEntryParameterNames.AUTOCENTER_OFFSET_AMU);
            autocenter_offset_amu.setValue("0.0");
            entry.getPar().add(autocenter_offset_amu);
            PrawnFile.Run.RunTable.Entry.Par countTimeSec = new PrawnFile.Run.RunTable.Entry.Par();
            countTimeSec.setName(RunTableEntryParameterNames.COUNT_TIME_SEC);
            countTimeSec.setValue("" + legacyRunTable.getCountTimeSec().get(i));
            entry.getPar().add(countTimeSec);
            PrawnFile.Run.RunTable.Entry.Par delay_sec = new PrawnFile.Run.RunTable.Entry.Par();
            delay_sec.setName(RunTableEntryParameterNames.DELAY_SEC);
            delay_sec.setValue("" + legacyRunTable.getDelaySec().get(i));
            entry.getPar().add(delay_sec);
            PrawnFile.Run.RunTable.Entry.Par collector_focus = new PrawnFile.Run.RunTable.Entry.Par();
            collector_focus.setName(RunTableEntryParameterNames.COLLECTOR_FOCUS);
            collector_focus.setValue("" + legacyRunTable.getCollectorFocus().get(i));
            entry.getPar().add(collector_focus);
            PrawnFile.Run.RunTable.Entry.Par centeringTimeSec = new PrawnFile.Run.RunTable.Entry.Par();
            centeringTimeSec.setName(RunTableEntryParameterNames.CENTERING_TIME_SEC);
            centeringTimeSec.setValue("" + legacyRunTable.getCenteringTimeSec().get(i));
            entry.getPar().add(centeringTimeSec);
            PrawnFile.Run.RunTable.Entry.Par centering_frequency = new PrawnFile.Run.RunTable.Entry.Par();
            centering_frequency.setName(RunTableEntryParameterNames.CENTERING_FREQUENCY);
            centering_frequency.setValue("" + legacyRunTable.getCenteringFrequency().get(i));
            entry.getPar().add(centering_frequency);
            PrawnFile.Run.RunTable.Entry.Par detector_selection = new PrawnFile.Run.RunTable.Entry.Par();
            detector_selection.setName(RunTableEntryParameterNames.DETECTOR_SELECTION);
            detector_selection.setValue("0.0");
            entry.getPar().add(detector_selection);
            PrawnFile.Run.RunTable.Entry.Par mc_lm_pos = new PrawnFile.Run.RunTable.Entry.Par();
            mc_lm_pos.setName(RunTableEntryParameterNames.MC_LM_POS);
            mc_lm_pos.setValue("-1.000");
            entry.getPar().add(mc_lm_pos);
            PrawnFile.Run.RunTable.Entry.Par mc_hm_pos = new PrawnFile.Run.RunTable.Entry.Par();
            mc_hm_pos.setName(RunTableEntryParameterNames.MC_HM_POS);
            mc_hm_pos.setValue("-1.000");
            entry.getPar().add(mc_hm_pos);
            PrawnFile.Run.RunTable.Entry.Par sc_reference = new PrawnFile.Run.RunTable.Entry.Par();
            sc_reference.setName(RunTableEntryParameterNames.SC_REFERENCE);
            sc_reference.setValue("" + legacyRunTable.getReference().get(i));
            entry.getPar().add(sc_reference);
            PrawnFile.Run.RunTable.Entry.Par sc_detector = new PrawnFile.Run.RunTable.Entry.Par();
            sc_detector.setName(RunTableEntryParameterNames.SC_DETECTOR);
            sc_detector.setValue("" + legacyRunTable.getDetector().get(i));
            entry.getPar().add(sc_detector);
            run.getRunTable().getEntry().add(entry);
        }
        // run.set
        // run.set parameters
        // run.set.scan
        // run.set.scan.measurement
        // run.set.scan.measurement.parameters
        // run.set.scan.measurement.data
        run.setSet(new PrawnFile.Run.Set());
        PrawnFile.Run.Set.Par date = new PrawnFile.Run.Set.Par();
        date.setName(SetParameterNames.DATE);
        date.setValue(legacyRun.getSet().getDate());
        run.getSet().getPar().add(date);
        PrawnFile.Run.Set.Par time = new PrawnFile.Run.Set.Par();
        time.setName(SetParameterNames.TIME);
        time.setValue(legacyRun.getSet().getTime());
        run.getSet().getPar().add(time);
        PrawnFile.Run.Set.Par qt1y = new PrawnFile.Run.Set.Par();
        qt1y.setName(SetParameterNames.QT_1_Y);
        qt1y.setValue("" + legacyRun.getSet().getQt1Y());
        run.getSet().getPar().add(qt1y);
        PrawnFile.Run.Set.Par qt1y_volts = new PrawnFile.Run.Set.Par();
        qt1y_volts.setName(SetParameterNames.QT_1_Y_VOLTS);
        qt1y_volts.setValue("0.0");
        run.getSet().getPar().add(qt1y_volts);
        PrawnFile.Run.Set.Par qt1z = new PrawnFile.Run.Set.Par();
        qt1z.setName(SetParameterNames.QT_1_Z);
        qt1z.setValue("0");
        run.getSet().getPar().add(qt1z);
        PrawnFile.Run.Set.Par pbm = new PrawnFile.Run.Set.Par();
        pbm.setName(SetParameterNames.PBM);
        pbm.setValue("" + legacyRun.getSet().getPbm());
        run.getSet().getPar().add(pbm);
        // the issue is that the legacy prawn file lists all the scans for a peak together
        // while the newer prawn file lists the scans for every peak together
        // so set up the Prawn data structure to populate
        List<PrawnFile.Run.Set.Scan> scanSet = run.getSet().getScan();
        scanSet.clear();
        for (int i = 0; i < legacyRun.getScans(); i++) {
            PrawnFile.Run.Set.Scan scan = new PrawnFile.Run.Set.Scan();
            scan.setNumber((short) (i + 1));
            scanSet.add(scan);
        }
        for (PrawnLegacyFile.Run.Set.Data.Peak legacyPeak : legacyRun.getSet().getData().getPeak()) {
            for (int i = 0; i < legacyPeak.getScan().size(); i++) {
                PrawnFile.Run.Set.Scan.Measurement measurement = makeMeasurement(legacyPeak.getScan().get(i), legacyPeak.getPeakName());
                scanSet.get(i).getMeasurement().add(measurement);
            }
        }
        prawnFile.getRun().add(run);
    }
    return prawnFile;
}

Example 4 with ShrimpDataFileInterface

use of org.cirdles.squid.shrimp.ShrimpDataFileInterface in project Squid by CIRDLES.

the class SquidProject method splitPrawnFileAtRun.

/**
 * Splits the current PrawnFile into two sets of runs based on the index of
 * the run supplied and writes out two prawn xml files in the same folder as
 * the original.
 *
 * @param run
 * @param useOriginalData, when true, the original unedited file is used,
 *                         otherwise the edited file is used.
 * @return String [2] containing the file names of the two Prawn XML files
 * written as a result of the split.
 */
public String[] splitPrawnFileAtRun(Run run, boolean useOriginalData) throws SquidException {
    String[] retVal = new String[2];
    retVal[0] = prawnFileHandler.getCurrentPrawnSourceFileLocation().replace(".xml", "-PART-A.xml").replace(".XML", "-PART-A.xml");
    retVal[1] = prawnFileHandler.getCurrentPrawnSourceFileLocation().replace(".xml", "-PART-B.xml").replace(".XML", "-PART-B.xml");
    // get index from original prawnFile
    int indexOfRun = prawnFile.getRun().indexOf(run);
    List<Run> runs = prawnFile.getRun();
    List<Run> runsCopy;
    if (useOriginalData) {
        ShrimpDataFileInterface prawnFileOriginal = null;
        try {
            prawnFileOriginal = deserializePrawnData();
            runsCopy = new CopyOnWriteArrayList<>(prawnFileOriginal.getRun());
        } catch (IOException | JAXBException | SAXException | SquidException iOException) {
            throw new SquidException(iOException.getMessage());
        }
    } else {
        runsCopy = new CopyOnWriteArrayList<>(runs);
    }
    List<Run> first = runsCopy.subList(0, indexOfRun);
    List<Run> second = runsCopy.subList(indexOfRun, runs.size());
    // keep first
    runs.clear();
    // preserve order
    for (Run runF : first) {
        runs.add(runF);
    }
    prawnFile.setRuns((short) runs.size());
    try {
        prawnFileHandler.writeRawDataFileAsXML(prawnFile, retVal[0]);
    } catch (IOException | JAXBException Exception) {
    }
    runs.clear();
    // preserve order
    for (Run runS : second) {
        runs.add(runS);
    }
    prawnFile.setRuns((short) runs.size());
    try {
        prawnFileHandler.writeRawDataFileAsXML(prawnFile, retVal[1]);
    } catch (IOException | JAXBException Exception) {
    }
    // restore list
    runs.clear();
    // preserve order
    for (Run runF : first) {
        runs.add(runF);
    }
    for (Run runS : second) {
        runs.add(runS);
    }
    prawnFile.setRuns((short) runs.size());
    return retVal;
}

Example 5 with ShrimpDataFileInterface

use of org.cirdles.squid.shrimp.ShrimpDataFileInterface in project Squid by CIRDLES.

the class SquidProject method setupPrawnXMLFileByJoin.

public boolean setupPrawnXMLFileByJoin(List<File> prawnXMLFilesNew) throws IOException, JAXBException, SAXException, SquidException {
    if (prawnXMLFilesNew.size() == 2) {
        ShrimpDataFileInterface prawnFile1 = prawnFileHandler.unmarshallPrawnFileXML(prawnXMLFilesNew.get(0).getCanonicalPath(), false);
        ShrimpDataFileInterface prawnFile2 = prawnFileHandler.unmarshallPrawnFileXML(prawnXMLFilesNew.get(1).getCanonicalPath(), false);
        if ((prawnFile1 != null) && (prawnFile2 != null)) {
            long start1 = PrawnFileUtilities.timeInMillisecondsOfRun(prawnFile1.getRun().get(0));
            long start2 = PrawnFileUtilities.timeInMillisecondsOfRun(prawnFile2.getRun().get(0));
            if (start1 > start2) {
                prawnFile2.getRun().addAll(prawnFile1.getRun());
                prawnFile2.setRuns((short) prawnFile2.getRun().size());
                prawnSourceFile = new File(prawnXMLFilesNew.get(1).getName().replace(".xml", "").replace(".XML", "") + "-JOIN-" + prawnXMLFilesNew.get(0).getName().replace(".xml", "").replace(".XML", "") + ".xml");
                prawnFile = prawnFile2;
            } else {
                prawnFile1.getRun().addAll(prawnFile2.getRun());
                prawnFile1.setRuns((short) prawnFile1.getRun().size());
                prawnSourceFile = new File(prawnXMLFilesNew.get(0).getName().replace(".xml", "").replace(".XML", "") + "-JOIN-" + prawnXMLFilesNew.get(1).getName().replace(".xml", "").replace(".XML", "") + ".xml");
                prawnFile = prawnFile1;
            }
            updatePrawnFileHandlerWithFileLocation();
            // write and read merged file to confirm conforms to schema
            serializePrawnData(prawnFileHandler.getCurrentPrawnSourceFileLocation());
            prawnFile = prawnFileHandler.unmarshallCurrentPrawnFileXML();
            removedRuns = new ArrayList<>();
            if (prawnFileExists()) {
                task.setPrawnFile(prawnFile);
                ((Task) task).setupSquidSessionSkeleton();
            }
        } else {
            prawnFile = null;
        }
    } else {
        throw new IOException("Two files not present");
    }
    return prawnFileExists();
}